I just chalk it up (in-universe, at least) to the Emperor being overcome with hubris at the moment he's torturing and trying to kill Luke with his Sith lightning. He's so engrossed in destroying this new, rebellious and uncooperative threat to his Empire that he doesn't sense Vader connecting with the good that's left within himself and becoming Anakin Skywalker once more.

When Anakin grabbed the Emperor to throw him down the reactor shaft he took his former Master completely by surprise. Palpatine could do little in his moment of surprise and shock other than start screaming and let his lightning bolts flail wildly out of control.

But if you want a real world explanation what CC said is what I subscribe to. Jedi was filmed more than 20 years before Sith and in the early eighties Lucas hadn't a clue how the Emperor would be portrayed in any prequel films....provided he ever got around to even making any of them.